Our Test Organism Drosophila simulans. Trait of Interest Red vs. White.
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Transcript of Our Test Organism Drosophila simulans. Trait of Interest Red vs. White.
Our Test OrganismDrosophila simulans
Trait of Interest
• Red vs. White
What did we do in lab 1?
• Vial of 5 white-eyed females• Vial of 6 males, 5 white-eyed
– With ONE red-eyed male mixed in– What is p(red-eye allele)?
• 1/11
• What did we say about the fitness of the red-eyed mutant?— Sensory perception— Should be more fit because has better vision— White eyes = reduced mate tracking
What should we expect to see?
• More or less red-eyed flies?• So we have an adaptive allele (red-eyed
mutation)…– Should increase in frequency.. What is this called?
• Selective sweep
– What about polymorphisms located near it?• Hitchhiking
• How can we tell if a sweep and hitchhiking has happened?
Genotype the flies near that gene!
• Need to first get DNA from the flies (DNA Isolation)
– Squish flies to release all their DNA
• Need to look at polymorphisms near that gene– Polymerase Chain Reaction
• Amplify the DNA of interest enough so we can look at it on a gel
Ahhh! Help meeeeeee
Drosophila chromosome
Red / Whiteeye color gene
“Near” “Far”
22 million bases of DNA
What are we going to look at?• Two markers on X-chromosome
o One close to the gene for white eyeso One far from the gene for white eyes
• Why are we going to look at 2 markers?
22 million bases of DNA
Polymorphisms
• Red: gene mutated to give flies red-eyes• Blue: indel polymorphism
– What is an indel polymorphism?– NEAR marker
• Yellow: indel polymorphism– FAR marker
Recombination Hotspot!
• Who is linked to the red gene?– Blue or yellow?
• Say that 1 red-eyed male in the first lab had:– Insertion at the near marker (blue)– Deletion at the far marker (yellow)
• All white-eyed individuals had:– Deletion at the near marker (blue)– Insertion at the far marker (yellow)
• What will our flies today look like at each marker?
Recombination Hotspot!
Hypothesis
This is called genetic hitchhiking
• As chromosomes are passed down over generations, they sometimes “trade pieces” with other chromosomes... (recombination)
• More likely to keep the same close neighbor gene variants than far away neighbors.
• If natural selection makes one variant spread quickly, itsclose neighbor variants may also spread.
Selective Sweep (positive directional selection)
Frequency in sample
# si
tes
1 2 3 4Frequency in sample
# si
tes
1 2 3 4
Advantageous mutation
Selective Sweep/HitchhikingBefore sweep After sweep
This is one chromosome from 12 different people. The different colors represent different alleles for that gene.
What happened?
Selective Sweep/Hitchhiking
• If a mutation is advantageous it will likely increase in frequency
• Why?• What will happen to genes/traits that are
closely linked to the advantageous mutation?
• What will happen to genes/traits that are not closely linked to the advantageous mutation?
Variation at 3 loci
• 2 variants at the eye color gene– Red & White alleles
• 2 variants at the Near marker– High and Low – The red-eyed male from Day 1 has the high allele at Near– The white eyed flies had both variants
• 2 variants at the Far marker– High and Low– The red-eyed male from Day 1 has the low allele at Far– The white eyed flies had both variants
• Sequence differences (aka variation) between alleles• Usually base pair repeats, insertions, or deletions• Used for between & within-species comparisons
How are we going to observe & measure genetic variation?- Microsatellite Markers -
“Genetic markers”Reference point in the genome with 2+ alleles
A sequence: AACATGGTGACGGCTAGCA
a sequence: AACATGGTGAGAGAGACGGCTAGCA
High allele
Low allele
How to tell males from females
• Males have black abdomens
• Look close at the tip of the male abdomen and you will see his junk
• Females have rounded abdomens
Female Male
Red male
Red female
White male
White female
Sexing your flies: males have a “black butt”, females have large white abdomen
Sexing
Female Male
A note about contamination
• DO NOT CONTAMINATE YOUR DNA ISOLATIONS!– Change tips in between EACH fly squish! – Just because you can’t see the DNA on the tip,
doesn’t mean it’s not there!